Although hydrologic models provide hypothesis testing of complex dynamics occurring at catchments, freshwater quality modeling is still incipient at many subtropical headwaters. In Brazil, a few modeling studies assess freshwater nutrients, limiting policies on hydrologic ecosystem services. This paper aims to compare freshwater quality scenarios under different land-use and land-cover (LULC) change, one of them related to ecosystem-based adaptation (EbA), in Brazilian headwaters. Using the spatially semi distributed Soil and Water Assessment Tool (SWAT) model, nitrate, total phosphorous (TP) and sediment were modeled in catchments ranging from 7.2 to 1037 km2. These headwaters were eligible areas of the Brazilian payment for ecosystem services (PES) projects in the Cantareira water supply system, which had supplied water to 9 million people in the São Paulo metropolitan region (SPMR). We considered SWAT modeling of three LULC scenarios: (i) recent past scenario (S1), with historical LULC in 1990; (ii) current land-use scenario (S2), with LULC for the period 2010–2015 with field validation; and (iii) future land-use scenario with PES (S2CEbA). This latter scenario proposed forest cover restoration through EbA following the river basin plan by 2035. These three LULC scenarios were tested with a selected record of rainfall and evapotranspiration observed in 2006–2014, with the occurrence of extreme droughts. To assess hydrologic services, we proposed the hydrologic service index (HSI), as a new composite metric comparing water pollution levels (WPL) for reference catchments, related to the grey water footprint (greyWF) and water yield. On the one hand, water quality simulations allowed for the regionalization of greyWF at spatial scales under LULC scenarios. According to the critical threshold, HSI identified areas as less or more sustainable catchments. On the other hand, conservation practices simulated through the S2CEbA scenario envisaged not only additional and viable best management practices (BMP), but also preventive decision-making at the headwaters of water supply systems.